ome-ngff-tools
The following versions of each viewer were used in testing:
- napari 0.4.16 with plugin napari-ome-zarr 0.5.2 and ome-zarr 0.6.0.
- Open via command line:
napari https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr - Use napari console to open additional image:
viewer.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")
- Open via command line:
- vizarr using current viewer October 2022. Open via URL - see example.
- MoBIE plugin for ImageJ/Fiji (mobie-viewer-fiji v2.2.1, mobie-io v2.0.7). See MoBIE guide for installation instructions and how to open Zarr files. Hint: Press
pto bring the rendering settings controls. - itkwidgets. Use in a python notebook, or open via URL: See example.
- neuroglancer.
- webKnossos version 24.03.0.
- OMERO with BioFormats ZarrReader 0.2.0.
NB: the N5-viewer, a Fiji plugin based on BigDataViewer, will also support OME-NGFF soon.
Key
| Feature supported | |
| Not supported (no effect) | |
| Image doesn't open correctly | |
| Not tested / not confirmed |
| feature | sample data | napari | vizarr | MoBIE | vtk-itk-viewer | neuroglancer | webknossos | OMERO |
|---|---|---|---|---|---|---|---|---|
Z downsample
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9836832.zarr
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omero info
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6001240.zarr
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multiscales downsampling not=2
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9846318.zarr/0
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axes (v0.3)
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9836998.zarr
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axes (v0.4)
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6001240.zarr
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labels
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5514375.zarr
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HCS plate
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idr0001
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bioformats2raw.layout
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9838562.zarr
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multiple 'multiscales'
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4995115.zarr
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scale within coordinateTransformations on datasets (v0.4)
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6001240.zarr
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translation within coordinateTransformations on datasets (v0.4)
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13457537.zarr
translate onto 13457227.zarr
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scale within coordinateTransformations on multiscales (v0.4)
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13457539.zarr
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translation within coordinateTransformations on multiscales (v0.4)
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13457539.zarr
translate onto 13457227.zarr
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overlay multiple images
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multiple Channels
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13457227.zarr
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multiple Time-points
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13457227.zarr
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